Imputation Report For Cohort: WTCCC_cohort

Per chromosome imputation report for cohort WTCCC_cohort.

Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

Cohort Metadata

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Information captured during the processing of this cohort.

Property Value
FORMAT MINIMAC2

UPLOADED 12.4.2021

Genome-Wide

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A: Alternate Allele Frequency: Genome-Wide

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 17883586 79.546
0.1 1221147 5.432
0.2 810985 3.607
0.3 617510 2.747
0.4 495321 2.203
0.5 405361 1.803
0.6 348819 1.552
0.7 290679 1.293
0.8 241173 1.073
0.9 167605 0.746
Total 22482186 100.000

B: Imputation INFO Score: Genome-Wide

Variants binned by imputation INFO score

INFO Score Count %
0.3 1367935 6.085
0.4 1630497 7.252
0.5 2131252 9.480
0.6 2760289 12.278
0.7 3277116 14.577
0.8 3534860 15.723
0.9 7750740 34.475
1.0 29497 0.131
Total 22482186 100.000

Chromosome 1

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1363728 79.9709
0.1 89352 5.2397
0.2 57866 3.3933
0.3 45395 2.6620
0.4 37499 2.1990
0.5 30402 1.7828
0.6 27078 1.5879
0.7 21694 1.2722
0.8 18605 1.0910
0.9 13661 0.8011
Total 1705280

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 104530 6.1298
0.4 126335 7.4085
0.5 163078 9.5631
0.6 212129 12.4395
0.7 252549 14.8098
0.8 269738 15.8178
0.9 574761 33.7048
1.0 2160 0.1267
Total 1705280

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 2

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1521939 80.2644
0.1 100514 5.3009
0.2 66172 3.4898
0.3 49378 2.6041
0.4 38639 2.0378
0.5 32735 1.7264
0.6 28710 1.5141
0.7 23365 1.2322
0.8 20136 1.0619
0.9 14570 0.7684
Total 1896158

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 107228 5.6550
0.4 129251 6.8165
0.5 171099 9.0235
0.6 229462 12.1014
0.7 281585 14.8503
0.8 302173 15.9361
0.9 672952 35.4903
1.0 2408 0.1270
Total 1896158

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 3

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1283134 79.8705
0.1 87675 5.4575
0.2 55282 3.4411
0.3 43175 2.6875
0.4 34872 2.1707
0.5 29254 1.8210
0.6 24710 1.5381
0.7 20480 1.2748
0.8 16581 1.0321
0.9 11355 0.7068
Total 1606518

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 89473 5.5694
0.4 106131 6.6063
0.5 143733 8.9469
0.6 193368 12.0365
0.7 237125 14.7602
0.8 257980 16.0583
0.9 576551 35.8882
1.0 2157 0.1343
Total 1606518

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 4

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1240741 79.0174
0.1 82050 5.2254
0.2 60614 3.8602
0.3 44901 2.8595
0.4 34088 2.1709
0.5 27850 1.7736
0.6 24426 1.5556
0.7 21621 1.3769
0.8 19860 1.2648
0.9 14062 0.8955
Total 1570213

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 89060 5.6718
0.4 105898 6.7442
0.5 141483 9.0104
0.6 186958 11.9065
0.7 227001 14.4567
0.8 249942 15.9177
0.9 568203 36.1864
1.0 1668 0.1062
Total 1570213

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 5

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1162069 79.8972
0.1 76955 5.2910
0.2 53080 3.6495
0.3 40328 2.7727
0.4 31697 2.1793
0.5 24614 1.6923
0.6 22361 1.5374
0.7 18267 1.2559
0.8 14955 1.0282
0.9 10129 0.6964
Total 1454455

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 81267 5.5875
0.4 95870 6.5915
0.5 127869 8.7915
0.6 171271 11.7756
0.7 211765 14.5597
0.8 233386 16.0463
0.9 530779 36.4933
1.0 2248 0.1546
Total 1454455

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 6

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1115699 78.9240
0.1 81743 5.7825
0.2 52786 3.7341
0.3 40174 2.8419
0.4 32778 2.3187
0.5 25751 1.8216
0.6 22684 1.6047
0.7 17077 1.2080
0.8 15205 1.0756
0.9 9741 0.6891
Total 1413638

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 72812 5.1507
0.4 85374 6.0393
0.5 116125 8.2146
0.6 158164 11.1884
0.7 199091 14.0836
0.8 224170 15.8577
0.9 555698 39.3098
1.0 2204 0.1559
Total 1413638

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 7

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 1005463 79.3690
0.1 69640 5.4972
0.2 47563 3.7545
0.3 35564 2.8073
0.4 28532 2.2523
0.5 23597 1.8627
0.6 18910 1.4927
0.7 16320 1.2883
0.8 12183 0.9617
0.9 9049 0.7143
Total 1266821

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 77010 6.0790
0.4 90495 7.1435
0.5 119327 9.4194
0.6 154921 12.2291
0.7 184826 14.5897
0.8 200664 15.8400
0.9 438268 34.5959
1.0 1310 0.1034
Total 1266821

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 8

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 992708 80.0723
0.1 64037 5.1653
0.2 44350 3.5773
0.3 32645 2.6332
0.4 27620 2.2278
0.5 21361 1.7230
0.6 19367 1.5622
0.7 15544 1.2538
0.8 13131 1.0592
0.9 9002 0.7261
Total 1239765

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 71751 5.7875
0.4 84039 6.7786
0.5 108521 8.7534
0.6 145481 11.7346
0.7 181951 14.6762
0.8 196112 15.8185
0.9 450260 36.3182
1.0 1650 0.1331
Total 1239765

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 9

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 753977 79.6899
0.1 53745 5.6805
0.2 34056 3.5995
0.3 24789 2.6200
0.4 20374 2.1534
0.5 15717 1.6612
0.6 14756 1.5596
0.7 11663 1.2327
0.8 9683 1.0234
0.9 7379 0.7799
Total 946139

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 52467 5.5454
0.4 62368 6.5918
0.5 84587 8.9402
0.6 114539 12.1059
0.7 140305 14.8292
0.8 154762 16.3572
0.9 335904 35.5026
1.0 1207 0.1276
Total 946139

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 10

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 881072 79.4987
0.1 61009 5.5048
0.2 39577 3.5710
0.3 28729 2.5922
0.4 24734 2.2317
0.5 20875 1.8835
0.6 16857 1.5210
0.7 14276 1.2881
0.8 12571 1.1343
0.9 8585 0.7746
Total 1108285

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 59700 5.3867
0.4 70566 6.3671
0.5 94129 8.4932
0.6 127331 11.4890
0.7 159015 14.3478
0.8 176982 15.9690
0.9 418531 37.7638
1.0 2031 0.1833
Total 1108285

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 11

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 868549 79.4186
0.1 59196 5.4128
0.2 36204 3.3104
0.3 30720 2.8090
0.4 24374 2.2287
0.5 20709 1.8936
0.6 17952 1.6415
0.7 14417 1.3183
0.8 12151 1.1111
0.9 9362 0.8560
Total 1093634

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 61522 5.6255
0.4 73032 6.6779
0.5 98616 9.0173
0.6 130943 11.9732
0.7 159241 14.5607
0.8 171313 15.6646
0.9 396572 36.2619
1.0 2395 0.2190
Total 1093634

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 12

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 838212 79.6281
0.1 57055 5.4201
0.2 35524 3.3747
0.3 30740 2.9202
0.4 22760 2.1621
0.5 18841 1.7898
0.6 16360 1.5542
0.7 12460 1.1837
0.8 12468 1.1844
0.9 8239 0.7827
Total 1052659

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 60443 5.7419
0.4 71868 6.8273
0.5 93218 8.8555
0.6 125299 11.9031
0.7 151097 14.3538
0.8 167225 15.8860
0.9 381869 36.2766
1.0 1640 0.1558
Total 1052659

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 13

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 624079 78.7205
0.1 42931 5.4153
0.2 28051 3.5383
0.3 22752 2.8699
0.4 17566 2.2158
0.5 15501 1.9553
0.6 12609 1.5905
0.7 11381 1.4356
0.8 9689 1.2222
0.9 8219 1.0367
Total 792778

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 41607 5.2483
0.4 49887 6.2927
0.5 68720 8.6683
0.6 93770 11.8280
0.7 117540 14.8263
0.8 129254 16.3039
0.9 290558 36.6506
1.0 1442 0.1819
Total 792778

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 14

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 555507 79.4550
0.1 38951 5.5712
0.2 26286 3.7597
0.3 18063 2.5836
0.4 15499 2.2168
0.5 11876 1.6986
0.6 10145 1.4511
0.7 9045 1.2937
0.8 7779 1.1126
0.9 5996 0.8576
Total 699147

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 41527 5.9397
0.4 50327 7.1983
0.5 65680 9.3943
0.6 86439 12.3635
0.7 101437 14.5087
0.8 108864 15.5710
0.9 244071 34.9098
1.0 802 0.1147
Total 699147

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 15

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 497379 79.6223
0.1 33362 5.3407
0.2 22368 3.5808
0.3 16706 2.6744
0.4 14279 2.2858
0.5 11781 1.8859
0.6 8956 1.4337
0.7 7909 1.2661
0.8 6557 1.0497
0.9 5376 0.8606
Total 624673

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 39694 6.3544
0.4 48588 7.7781
0.5 63162 10.1112
0.6 79441 12.7172
0.7 92256 14.7687
0.8 97455 15.6010
0.9 203165 32.5234
1.0 912 0.1460
Total 624673

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 16

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 531407 79.5658
0.1 37800 5.6597
0.2 22841 3.4199
0.3 19144 2.8664
0.4 13968 2.0914
0.5 12145 1.8184
0.6 10688 1.6003
0.7 9490 1.4209
0.8 6365 0.9530
0.9 4036 0.6043
Total 667884

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 46776 7.0036
0.4 55760 8.3488
0.5 71138 10.6513
0.6 87937 13.1665
0.7 99471 14.8935
0.8 106750 15.9833
0.9 199621 29.8886
1.0 431 0.0645
Total 667884

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 17

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 450966 79.2172
0.1 30181 5.3016
0.2 23026 4.0448
0.3 15475 2.7184
0.4 13550 2.3802
0.5 11131 1.9553
0.6 8798 1.5455
0.7 7907 1.3890
0.8 5654 0.9932
0.9 2590 0.4550
Total 569278

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 50109 8.8022
0.4 59949 10.5307
0.5 73375 12.8891
0.6 81629 14.3390
0.7 83371 14.6450
0.8 83580 14.6818
0.9 136987 24.0633
1.0 278 0.0488
Total 569278

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 18

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 488739 79.0812
0.1 33938 5.4914
0.2 23458 3.7957
0.3 17664 2.8582
0.4 13891 2.2477
0.5 11068 1.7909
0.6 9492 1.5359
0.7 8001 1.2946
0.8 6588 1.0660
0.9 5183 0.8386
Total 618022

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 36980 5.9836
0.4 45052 7.2897
0.5 61223 9.9063
0.6 79381 12.8444
0.7 91885 14.8676
0.8 97383 15.7572
0.9 205454 33.2438
1.0 664 0.1074
Total 618022

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 19

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 330738 77.5563
0.1 28370 6.6526
0.2 18677 4.3797
0.3 12922 3.0301
0.4 9596 2.2502
0.5 8211 1.9254
0.6 6667 1.5634
0.7 5766 1.3521
0.8 3920 0.9192
0.9 1582 0.3710
Total 426449

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 48173 11.2963
0.4 55115 12.9242
0.5 60871 14.2739
0.6 61150 14.3393
0.7 57222 13.4183
0.8 57067 13.3819
0.9 86635 20.3154
1.0 216 0.0507
Total 426449

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 20

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 390563 79.5883
0.1 27273 5.5576
0.2 18086 3.6855
0.3 13442 2.7392
0.4 11179 2.2780
0.5 8901 1.8138
0.6 7648 1.5585
0.7 5973 1.2172
0.8 4655 0.9486
0.9 3009 0.6132
Total 490729

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 31992 6.5193
0.4 39651 8.0800
0.5 52008 10.5981
0.6 65353 13.3175
0.7 71748 14.6207
0.8 74778 15.2381
0.9 154727 31.5300
1.0 472 0.0962
Total 490729

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 21

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 225870 78.1430
0.1 15736 5.4441
0.2 10151 3.5119
0.3 9027 3.1230
0.4 7217 2.4968
0.5 5965 2.0637
0.6 4875 1.6866
0.7 4482 1.5506
0.8 4000 1.3839
0.9 1724 0.5964
Total 289047

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 19731 6.8262
0.4 23407 8.0980
0.5 31530 10.9083
0.6 39021 13.4999
0.7 42242 14.6142
0.8 42875 14.8332
0.9 89821 31.0749
1.0 420 0.1453
Total 289047

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome 22

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 219380 78.6055
0.1 15903 5.6982
0.2 11130 3.9880
0.3 7945 2.8468
0.4 6913 2.4770
0.5 5239 1.8772
0.6 4687 1.6794
0.7 3909 1.4006
0.8 2593 0.9291
0.9 1391 0.4984
Total 279090

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 23538 8.4338
0.4 27546 9.8699
0.5 33626 12.0484
0.6 39683 14.2187
0.7 40110 14.3717
0.8 40153 14.3871
0.9 74253 26.6054
1.0 181 0.0649
Total 279090

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering

Chromosome X

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A: Alternate Allele Frequency vs HRC

Plot of the Alt Allele frequency in cohort vs HRC

B: Alternate Allele Frequency

Bar chart displaying variants binned by alternate allele frequency

C: Alternate Allele Frequency

Variants binned by alternate allele frequency

Alt Allele Frq Count %
0.0 541667 80.6623
0.1 33731 5.0231
0.2 23837 3.5497
0.3 17832 2.6555
0.4 13696 2.0395
0.5 11837 1.7627
0.6 10083 1.5015
0.7 9632 1.4343
0.8 5844 0.8703
0.9 3365 0.5011
Total 671524

D: Imputation INFO Score

Variants binned by imputation INFO score

E: Imputation INFO Score

Bar chart displaying binned by imputation INFO score

INFO Score Count %
0.3 60545 9.0161
0.4 73988 11.0179
0.5 88134 13.1245
0.6 96619 14.3880
0.7 94283 14.0402
0.8 92254 13.7380
0.9 165100 24.5859
1.0 601 0.0895
Total 671524

F: Imputation INFO Score

Manhattan plot of the INFO score across the chromosome

G: Order of Chr/Pos

To check for consistent ascending Chr/Pos ordering